I am trying to represent a variable that is set by a user that effects the cost of an item. The same variable would show on each applicable item block. Block may or may not be stacked as in the image (the grey box could be in between the green box). Is there a better way to represent this variable item amount?
How about indicating with an asterisk or an icon of similar meaning like (!) or (?) next to the cost, to show that it is being affected by a separate/global entity. This would be similar to a page note, for which a reader can look up additional information if they choose. Or use an icon that has some meaning associated with the variable.
Upon hovering over or clicking on the icon and/or the cost, you could either show the variable underneath, or display a global contextual info box that houses the variable and any related info. You could let the user change the variable from this global box, thereby updating all the visible costs in real time.
Seems like the issue is the use of the boxes/buttons to represent data points that could just be text, and as text would take up less space and be less prone to creating the visual noise you talked about.
I've given it the label "Metadata" but it could be something less technical, and I've made each item a simple link, but you could utilize other selection methods as you required.
There's a feature similar to this in an app I'm working on and I call it a "Stat Drawer" (because it slides out, and has stats) The idea is the same: Create an area in the UI that can handle a variety of textual information (and a small amount of interaction).